closure: Closure tests
In secr: Spatially Explicit Capture-Recapture

closure.test

R Documentation

Closure tests

Description

Perform tests to determine whether a population sampled by capture-recapture is closed to gains and losses over the period of sampling.

Usage


closure.test(object, SB = FALSE, min.expected = 2)

Arguments

`object`	`capthist` object
`SB`	logical, if TRUE then test of Stanley and Burnham 1999 is calculated in addition to that of Otis et al. 1978
`min.expected`	integer for the minimum expected count in any cell of a component 2x2 table

Details

The test of Stanley and Burnham in part uses a sum over 2x2 contingency tables; any table with a cell whose expected count is less than min.expected is dropped from the sum. The default value of 2 is that used by CloseTest (Stanley and Richards 2005, T. Stanley pers. comm.; see also Stanley and Burnham 1999 p. 203).

Value

In the case of a single-session capthist object, either a vector with the statistic (z-value) and p-value for the test of Otis et al. (1978 p. 120) or a list whose components are data frames with the statistics and p-values for various tests and test components as follows –

`Otis`	Test of Otis et al. 1978
`Xc`	Overall test of Stanley and Burnham 1999
`NRvsJS`	Stanley and Burnham 1999
`NMvsJS`	Stanley and Burnham 1999
`MtvsNR`	Stanley and Burnham 1999
`MtvsNM`	Stanley and Burnham 1999
`compNRvsJS`	Occasion-specific components of NRvsJS
`compNMvsJS`	Occasion-specific components of NMvsJS

Check the original papers for an explanation of the components of the Stanley and Burnham test.

In the case of a multi-session object, a list with one component (as above) for each session.

Note

No omnibus test exists for closure: the existing tests may indicate nonclosure even when a population is closed if other effects such as trap response are present (see White et al. 1982 pp 96–97). The test of Stanley and Burnham is sensitive to individual heterogeneity which is inevitable in most spatial sampling, and it should not in general be used for this sort of data.

References

Otis, D. L., Burnham, K. P., White, G. C. and Anderson, D. R. (1978) Statistical inference from capture data on closed animal populations. Wildlife Monographs 62, 1–135.

Stanley, T. R. and Burnham, K. P. (1999) A closure test for time-specific capture–recapture data. Environmental and Ecological Statistics 6, 197–209.

Stanley, T. R. and Richards, J. D. (2005) A program for testing capture–recapture data for closure. Wildlife Society Bulletin 33, 782–785.

White, G. C., Anderson, D. R., Burnham, K. P. and Otis, D. L. (1982) Capture-recapture and removal methods for sampling closed populations. Los Alamos National Laboratory, Los Alamos, New Mexico.